title: ePMV embeds molecular modeling into professional animation software environments.
abstract: Increasingly complex research has made it more difficult to prepare data for publication, education, and outreach. Many scientists must also wade through black-box code to interface computational algorithms from diverse sources to supplement their bench work. To reduce these barriers we have developed an open-source plug-in, embedded Python Molecular Viewer (ePMV), that runs molecular modeling software directly inside of professional 3D animation applications (hosts) to provide simultaneous access to the capabilities of these newly connected systems. Uniting host and scientific algorithms into a single interface allows users from varied backgrounds to assemble professional quality visuals and to perform computational experiments with relative ease. By enabling easy exchange of algorithms, ePMV can facilitate interdisciplinary research, smooth communication between broadly diverse specialties, and provide a common platform to frame and visualize the increasingly detailed intersection(s) of cellular and molecular biology.
authors.affiliation: Molecular Biology, The Scripps Research Institute, La Jolla, CA 92037, USA.
authors.forename: Graham T
authors.initials: GT
authors.lastname: Johnson
authors.forename: Ludovic
authors.initials: L
authors.lastname: Autin
authors.forename: David S
authors.initials: DS
authors.lastname: Goodsell
authors.forename: Michel F
authors.initials: MF
authors.lastname: Sanner
authors.forename: Arthur J
authors.initials: AJ
authors.lastname: Olson
mesh_terms: D000465:Algorithms; D000818:Animals; D019295:Computational Biology / Q000295:instrumentation* / Q000379:methods; D003196:Computer Graphics; D006801:Humans; D021621:Imaging, Three-Dimensional / Q000295:instrumentation / Q000379:methods; D033183:Interdisciplinary Communication; D051379:Mice; D008958:Models, Molecular; D008967:Molecular Biology / Q000193:education; D008968:Molecular Conformation; D056004:Molecular Dynamics Simulation; D012984:Software; D014584:User-Computer Interface